return colour;
}
- @Override
- public int findColourInt(char symbol, int position, SequenceI seq)
- {
- if (colourScheme == null)
- {
- return -1;// Color.white; // Colour is 'None'
- }
-
- /*
- * get 'base' colour
- */
- ProfileI profile = consensus == null ? null : consensus.get(position);
- String modalResidue = profile == null ? null
- : profile.getModalResidue();
- float pid = profile == null ? 0f
- : profile.getPercentageIdentity(ignoreGaps);
- int colour = colourScheme
- .findColour(symbol, position, seq, modalResidue, pid).getRGB();
-
- /*
- * apply PID threshold and consensus fading if in force
- */
- if (!Comparison.isGap(symbol))
- {
- colour = adjustColourInt(symbol, position, colour);
- }
-
- return colour;
- }
-
/**
* Adjusts colour by applying thresholding or conservation shading, if in
* force. That is
return colour;
}
- protected int adjustColourInt(char symbol, int column, int colour)
- {
- if (!aboveThreshold(symbol, column))
- {
- colour = -1;// Color.white;
- }
-
- if (conservationColouring)
- {
- colour = applyConservationInt(colour, column);
- }
- return colour;
- }
-
/**
* Answers true if there is a consensus profile for the specified column, and
* the given residue matches the consensus (or joint consensus) residue for
return ColorUtils.bleachColour(currentColour, bleachFactor);
}
- protected int applyConservationInt(int currentColour, int column)
- {
- if (conservation == null || conservation.length <= column)
- {
- return currentColour;
- }
- char conservationScore = conservation[column];
-
- /*
- * if residues are fully conserved (* or 11), or all properties
- * are conserved (+ or 10), leave colour unchanged
- */
- if (conservationScore == '*' || conservationScore == '+'
- || conservationScore == (char) 10
- || conservationScore == (char) 11)
- {
- return currentColour;
- }
-
- if (Comparison.isGap(conservationScore))
- {
- return -1;// Color.white;
- }
-
- /*
- * convert score 0-9 to a bleaching factor 1.1 - 0.2
- */
- float bleachFactor = (11 - (conservationScore - '0')) / 10f;
-
- /*
- * scale this up by 0-5 (percentage slider / 20)
- * as a result, scores of: 0 1 2 3 4 5 6 7 8 9
- * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
- */
- bleachFactor *= (conservationIncrement / 20f);
-
- return ColorUtils.bleachColourInt(currentColour, bleachFactor);
- }
-
/**
* @see jalview.renderer.ResidueShaderI#getColourScheme()
*/